FailedConsole Output

Skipping 5,747 KB.. Full Log
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-filtering/1.0-beta-2/maven-filtering-1.0-beta-2.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-interpolation/1.6/plexus-interpolation-1.6.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-active-collections/1.0-beta-2/plexus-active-collections-1.0-beta-2.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-container-default/1.0-alpha-22/plexus-container-default-1.0-alpha-22.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-containers/1.0-alpha-22/plexus-containers-1.0-alpha-22.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-plugin-api/2.0.4/maven-plugin-api-2.0.4.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven/2.0.4/maven-2.0.4.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-settings/2.0.4/maven-settings-2.0.4.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-model/2.0.4/maven-model-2.0.4.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-profile/2.0.4/maven-profile-2.0.4.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-repository-metadata/2.0.4/maven-repository-metadata-2.0.4.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact/2.0.4/maven-artifact-2.0.4.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-archiver/2.4/maven-archiver-2.4.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-archiver/1.0-alpha-11/plexus-archiver-1.0-alpha-11.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-container-default/1.0-alpha-15/plexus-container-default-1.0-alpha-15.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-containers/1.0-alpha-15/plexus-containers-1.0-alpha-15.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-component-api/1.0-alpha-15/plexus-component-api-1.0-alpha-15.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-classworlds/1.2-alpha-6/plexus-classworlds-1.2-alpha-6.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-io/1.0-alpha-3/plexus-io-1.0-alpha-3.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-component-api/1.0-alpha-16/plexus-component-api-1.0-alpha-16.pom
Progress (1): 2.2 kB
                    
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-containers/1.0-alpha-16/plexus-containers-1.0-alpha-16.pom
Progress (1): 1.9 kB
                    
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/1.4.9/plexus-utils-1.4.9.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/2.0.1/plexus-utils-2.0.1.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus/2.0.3/plexus-2.0.3.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-repository-builder/1.0-alpha-2/maven-repository-builder-1.0-alpha-2.pom
Progress (1): 3.2 kB
                    
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-common-artifact-filters/1.0-alpha-1/maven-common-artifact-filters-1.0-alpha-1.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-components/6/maven-shared-components-6.pom
Progress (1): 3.1 kB
                    
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-common-artifact-filters/1.1/maven-common-artifact-filters-1.1.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-interpolation/1.7/plexus-interpolation-1.7.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-plugin-testing-harness/1.1/maven-plugin-testing-harness-1.1.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/file-management/1.1/file-management-1.1.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-archiver/1.0-alpha-12/plexus-archiver-1.0-alpha-12.jar
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-io/1.1/maven-shared-io-1.1.jar
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Progress (4): 31 kB | 49/177 kB | 41/51 kB | 4.1/39 kB
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Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/file-management/1.1/file-management-1.1.jar (31 kB at 1.7 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-repository-metadata/2.0.2/maven-repository-metadata-2.0.2.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact-manager/2.0.2/maven-artifact-manager-2.0.2.jar
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Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-io/1.1/maven-shared-io-1.1.jar (39 kB at 1.5 MB/s)
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/wagon/wagon-provider-api/1.0-alpha-6/wagon-provider-api-1.0-alpha-6.jar
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Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-interpolation/1.7/plexus-interpolation-1.7.jar (51 kB at 1.7 MB/s)
Progress (3): 119/177 kB | 25/49 kB | 20 kB
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-filtering/1.0-beta-2/maven-filtering-1.0-beta-2.jar
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Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-repository-metadata/2.0.2/maven-repository-metadata-2.0.2.jar (20 kB at 616 kB/s)
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Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact-manager/2.0.2/maven-artifact-manager-2.0.2.jar (49 kB at 1.3 MB/s)
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-plugin-parameter-documenter/2.0.6/maven-plugin-parameter-documenter-2.0.6.jar
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[INFO] Reading assembly descriptor: src/main/assembly/assembly.xml
[INFO] Building tar : /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.6/label/ubuntu/mango-distribution/target/mango-distribution-spark3_2.11-0.0.6-SNAPSHOT-bin.tar.gz
[WARNING] Entry: mango-distribution-spark3_2.11-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.11-0.0.6-SNAPSHOT-javadoc.jar longer than 100 characters.
[WARNING] Resulting tar file can only be processed successfully by GNU compatible tar commands
[WARNING] Entry: mango-distribution-spark3_2.11-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.11-0.0.6-SNAPSHOT-sources.jar longer than 100 characters.
[INFO] Building tar : /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.6/label/ubuntu/mango-distribution/target/mango-distribution-spark3_2.11-0.0.6-SNAPSHOT-bin.tar.bz2
[WARNING] Entry: mango-distribution-spark3_2.11-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.11-0.0.6-SNAPSHOT-javadoc.jar longer than 100 characters.
[WARNING] Resulting tar file can only be processed successfully by GNU compatible tar commands
[WARNING] Entry: mango-distribution-spark3_2.11-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.11-0.0.6-SNAPSHOT-sources.jar longer than 100 characters.
[INFO] Building zip: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.6/label/ubuntu/mango-distribution/target/mango-distribution-spark3_2.11-0.0.6-SNAPSHOT-bin.zip
[INFO] 
[INFO] -----------< org.bdgenomics.mango:mango-parent-spark3_2.11 >------------
[INFO] Building mango_2.11 0.0.6-SNAPSHOT                                 [5/5]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent-spark3_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent-spark3_2.11 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-parent-spark3_2.11 ---
[INFO] Modified 0 of 41 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-parent-spark3_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-parent-spark3_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-parent-spark3_2.11 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-parent-spark3_2.11 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-parent-spark3_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent-spark3_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent-spark3_2.11 ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-parent-spark3_2.11 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-parent-spark3_2.11 ---
[INFO] No source files found
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for mango_2.11 0.0.6-SNAPSHOT:
[INFO] 
[INFO] mango_2.11: CORE ................................... SUCCESS [ 24.103 s]
[INFO] mango_2.11: CLI .................................... SUCCESS [ 24.500 s]
[INFO] Mango_2.11: Assembly ............................... SUCCESS [ 21.195 s]
[INFO] mango_2.11: Distribution ........................... SUCCESS [01:05 min]
[INFO] mango_2.11 ......................................... SUCCESS [  0.978 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  02:16 min
[INFO] Finished at: 2020-08-16T22:16:10Z
[INFO] ------------------------------------------------------------------------

# make sure that the distribution package contains an assembly jar
# if no assembly jar is found, this will exit with code 1 and fail the build
tar tzf mango-distribution/target/mango-distribution*-bin.tar.gz | \
    grep mango-assembly | \
    grep jar | \
    grep -v -e sources -e javadoc
+ grep mango-assembly
+ tar tzf mango-distribution/target/mango-distribution-spark3_2.11-0.0.6-SNAPSHOT-bin.tar.gz
+ grep jar
+ grep -v -e sources -e javadoc
mango-distribution-spark3_2.11-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.11-0.0.6-SNAPSHOT.jar

# we are done with maven, so clean up the maven temp dir
find ${MANGO_MVN_TMP_DIR}
+ find /tmp/mangoTestMvndcjoHak
/tmp/mangoTestMvndcjoHak
/tmp/mangoTestMvndcjoHak/fake-7487462059346034234.txt
/tmp/mangoTestMvndcjoHak/fake-7100475595589873608.txt
/tmp/mangoTestMvndcjoHak/TempSuite592495430299786528.adam
/tmp/mangoTestMvndcjoHak/TempSuite592495430299786528.adam/._SUCCESS.crc
/tmp/mangoTestMvndcjoHak/TempSuite592495430299786528.adam/_processingSteps.avro
/tmp/mangoTestMvndcjoHak/TempSuite592495430299786528.adam/referenceName=2
/tmp/mangoTestMvndcjoHak/TempSuite592495430299786528.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvndcjoHak/TempSuite592495430299786528.adam/referenceName=2/positionBin=189/.part-00000-23017286-930d-497b-b623-7b06f69357c5.c000.snappy.parquet.crc
/tmp/mangoTestMvndcjoHak/TempSuite592495430299786528.adam/referenceName=2/positionBin=189/part-00000-23017286-930d-497b-b623-7b06f69357c5.c000.snappy.parquet
/tmp/mangoTestMvndcjoHak/TempSuite592495430299786528.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvndcjoHak/TempSuite592495430299786528.adam/_partitionedByStartPos
/tmp/mangoTestMvndcjoHak/TempSuite592495430299786528.adam/._references.avro.crc
/tmp/mangoTestMvndcjoHak/TempSuite592495430299786528.adam/_SUCCESS
/tmp/mangoTestMvndcjoHak/TempSuite592495430299786528.adam/._processingSteps.avro.crc
/tmp/mangoTestMvndcjoHak/TempSuite592495430299786528.adam/_references.avro
/tmp/mangoTestMvndcjoHak/TempSuite592495430299786528.adam/_readGroups.avro
/tmp/mangoTestMvndcjoHak/TempSuite592495430299786528.adam/._readGroups.avro.crc
/tmp/mangoTestMvndcjoHak/TempSuite592495430299786528.adam/referenceName=1
/tmp/mangoTestMvndcjoHak/TempSuite592495430299786528.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvndcjoHak/TempSuite592495430299786528.adam/referenceName=1/positionBin=240/.part-00000-23017286-930d-497b-b623-7b06f69357c5.c000.snappy.parquet.crc
/tmp/mangoTestMvndcjoHak/TempSuite592495430299786528.adam/referenceName=1/positionBin=240/part-00000-23017286-930d-497b-b623-7b06f69357c5.c000.snappy.parquet
/tmp/mangoTestMvndcjoHak/TempSuite592495430299786528.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvndcjoHak/TempSuite592495430299786528.adam/referenceName=1/positionBin=26/.part-00000-23017286-930d-497b-b623-7b06f69357c5.c000.snappy.parquet.crc
/tmp/mangoTestMvndcjoHak/TempSuite592495430299786528.adam/referenceName=1/positionBin=26/part-00000-23017286-930d-497b-b623-7b06f69357c5.c000.snappy.parquet
/tmp/mangoTestMvndcjoHak/invalidBuild.genome1887302519502826816
/tmp/mangoTestMvndcjoHak/invalidBuild.genome1887302519502826816/properties.txt
/tmp/mangoTestMvndcjoHak/TempSuite8412393407439245941.adam
/tmp/mangoTestMvndcjoHak/TempSuite8412393407439245941.adam/._samples.avro.crc
/tmp/mangoTestMvndcjoHak/TempSuite8412393407439245941.adam/._SUCCESS.crc
/tmp/mangoTestMvndcjoHak/TempSuite8412393407439245941.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvndcjoHak/TempSuite8412393407439245941.adam/_partitionedByStartPos
/tmp/mangoTestMvndcjoHak/TempSuite8412393407439245941.adam/._references.avro.crc
/tmp/mangoTestMvndcjoHak/TempSuite8412393407439245941.adam/_SUCCESS
/tmp/mangoTestMvndcjoHak/TempSuite8412393407439245941.adam/_references.avro
/tmp/mangoTestMvndcjoHak/TempSuite8412393407439245941.adam/._header.crc
/tmp/mangoTestMvndcjoHak/TempSuite8412393407439245941.adam/_samples.avro
/tmp/mangoTestMvndcjoHak/TempSuite8412393407439245941.adam/referenceName=1
/tmp/mangoTestMvndcjoHak/TempSuite8412393407439245941.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvndcjoHak/TempSuite8412393407439245941.adam/referenceName=1/positionBin=0/.part-00000-5b5eaec9-755d-4cbe-9980-adb3f35dd997.c000.snappy.parquet.crc
/tmp/mangoTestMvndcjoHak/TempSuite8412393407439245941.adam/referenceName=1/positionBin=0/part-00000-5b5eaec9-755d-4cbe-9980-adb3f35dd997.c000.snappy.parquet
/tmp/mangoTestMvndcjoHak/TempSuite8412393407439245941.adam/_header
/tmp/mangoTestMvndcjoHak/mmbroken1940472872153120678.genome
/tmp/mangoTestMvndcjoHak/invalidBuild.genome2136498663311510183
/tmp/mangoTestMvndcjoHak/invalidBuild.genome2136498663311510183/properties.txt
/tmp/mangoTestMvndcjoHak/TempSuite4316854463926459911
/tmp/mangoTestMvndcjoHak/genomes8998806834405716782
/tmp/mangoTestMvndcjoHak/genomes8998806834405716782/hg19.genome
/tmp/mangoTestMvndcjoHak/snappy-1.0.5-libsnappyjava.so
/tmp/mangoTestMvndcjoHak/genomes814284810998537834
/tmp/mangoTestMvndcjoHak/genomes814284810998537834/hg19.genome
/tmp/mangoTestMvndcjoHak/TempSuite4316854463926459911.adam
/tmp/mangoTestMvndcjoHak/TempSuite4316854463926459911.adam/._samples.avro.crc
/tmp/mangoTestMvndcjoHak/TempSuite4316854463926459911.adam/._SUCCESS.crc
/tmp/mangoTestMvndcjoHak/TempSuite4316854463926459911.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvndcjoHak/TempSuite4316854463926459911.adam/_partitionedByStartPos
/tmp/mangoTestMvndcjoHak/TempSuite4316854463926459911.adam/._references.avro.crc
/tmp/mangoTestMvndcjoHak/TempSuite4316854463926459911.adam/_SUCCESS
/tmp/mangoTestMvndcjoHak/TempSuite4316854463926459911.adam/_references.avro
/tmp/mangoTestMvndcjoHak/TempSuite4316854463926459911.adam/._header.crc
/tmp/mangoTestMvndcjoHak/TempSuite4316854463926459911.adam/_samples.avro
/tmp/mangoTestMvndcjoHak/TempSuite4316854463926459911.adam/referenceName=1
/tmp/mangoTestMvndcjoHak/TempSuite4316854463926459911.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvndcjoHak/TempSuite4316854463926459911.adam/referenceName=1/positionBin=0/.part-00000-cd890d5f-9fdd-4e81-9f52-cf0e98d64c28.c000.snappy.parquet.crc
/tmp/mangoTestMvndcjoHak/TempSuite4316854463926459911.adam/referenceName=1/positionBin=0/part-00000-cd890d5f-9fdd-4e81-9f52-cf0e98d64c28.c000.snappy.parquet
/tmp/mangoTestMvndcjoHak/TempSuite4316854463926459911.adam/_header
/tmp/mangoTestMvndcjoHak/2397347803626778017
/tmp/mangoTestMvndcjoHak/2397347803626778017/anoGam1.genome
/tmp/mangoTestMvndcjoHak/TempSuite8832967547100006570
/tmp/mangoTestMvndcjoHak/6573602042820896437
/tmp/mangoTestMvndcjoHak/TempSuite8832967547100006570.adam
/tmp/mangoTestMvndcjoHak/TempSuite8832967547100006570.adam/._SUCCESS.crc
/tmp/mangoTestMvndcjoHak/TempSuite8832967547100006570.adam/_processingSteps.avro
/tmp/mangoTestMvndcjoHak/TempSuite8832967547100006570.adam/referenceName=2
/tmp/mangoTestMvndcjoHak/TempSuite8832967547100006570.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvndcjoHak/TempSuite8832967547100006570.adam/referenceName=2/positionBin=189/.part-00000-838db8f0-f6a0-4151-9dda-cc54868cb059.c000.snappy.parquet.crc
/tmp/mangoTestMvndcjoHak/TempSuite8832967547100006570.adam/referenceName=2/positionBin=189/part-00000-838db8f0-f6a0-4151-9dda-cc54868cb059.c000.snappy.parquet
/tmp/mangoTestMvndcjoHak/TempSuite8832967547100006570.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvndcjoHak/TempSuite8832967547100006570.adam/_partitionedByStartPos
/tmp/mangoTestMvndcjoHak/TempSuite8832967547100006570.adam/._references.avro.crc
/tmp/mangoTestMvndcjoHak/TempSuite8832967547100006570.adam/_SUCCESS
/tmp/mangoTestMvndcjoHak/TempSuite8832967547100006570.adam/._processingSteps.avro.crc
/tmp/mangoTestMvndcjoHak/TempSuite8832967547100006570.adam/_references.avro
/tmp/mangoTestMvndcjoHak/TempSuite8832967547100006570.adam/_readGroups.avro
/tmp/mangoTestMvndcjoHak/TempSuite8832967547100006570.adam/._readGroups.avro.crc
/tmp/mangoTestMvndcjoHak/TempSuite8832967547100006570.adam/referenceName=1
/tmp/mangoTestMvndcjoHak/TempSuite8832967547100006570.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvndcjoHak/TempSuite8832967547100006570.adam/referenceName=1/positionBin=240/.part-00000-838db8f0-f6a0-4151-9dda-cc54868cb059.c000.snappy.parquet.crc
/tmp/mangoTestMvndcjoHak/TempSuite8832967547100006570.adam/referenceName=1/positionBin=240/part-00000-838db8f0-f6a0-4151-9dda-cc54868cb059.c000.snappy.parquet
/tmp/mangoTestMvndcjoHak/TempSuite8832967547100006570.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvndcjoHak/TempSuite8832967547100006570.adam/referenceName=1/positionBin=26/.part-00000-838db8f0-f6a0-4151-9dda-cc54868cb059.c000.snappy.parquet.crc
/tmp/mangoTestMvndcjoHak/TempSuite8832967547100006570.adam/referenceName=1/positionBin=26/part-00000-838db8f0-f6a0-4151-9dda-cc54868cb059.c000.snappy.parquet
/tmp/mangoTestMvndcjoHak/fake-8749905843914016868.sh
/tmp/mangoTestMvndcjoHak/TempSuite592495430299786528
/tmp/mangoTestMvndcjoHak/mmbroken71273519785035404.genome
/tmp/mangoTestMvndcjoHak/5486362855098016471
/tmp/mangoTestMvndcjoHak/5486362855098016471/anoGam1.genome
/tmp/mangoTestMvndcjoHak/308604735340687719
/tmp/mangoTestMvndcjoHak/fake-6207462812767786402.sh
/tmp/mangoTestMvndcjoHak/TempSuite8412393407439245941
rm -rf ${MANGO_MVN_TMP_DIR}
+ rm -rf /tmp/mangoTestMvndcjoHak

find . -name pom.xml \
    -exec sed -i.bak \
    -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${MANGO_MVN_TMP_DIR}:sun.io.serialization.extendedDebugInfo=true:g" \
    {} \;
+ find . -name pom.xml -exec sed -i.bak -e 's:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=/tmp/mangoTestMvndcjoHak:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

# set spark artifact string for downloading assembly
SPARK=spark-${SPARK_VERSION}
+ SPARK=spark-2.4.6

# what hadoop version are we on? format string for downloading spark assembly
if [[ $HADOOP_VERSION =~ ^2\.7 ]]; then
    HADOOP=hadoop2.7
else
    echo "Unknown Hadoop version."
    exit 1
fi
+ [[ 2.7.5 =~ ^2\.7 ]]
+ HADOOP=hadoop2.7

# Spark 2.4.3+ and less than 3.0.0 needs special case for Scala 2.12
if [ ${SCALAVER} == 2.12 ] && [ ${SPARK_VERSION} == 2.4.6 ]
then
    curl \
        -L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/${SPARK}/${SPARK}-bin-without-hadoop-scala-2.12.tgz" \
        -o ${MANGO_TMP_DIR}/${SPARK}-bin-without-hadoop-scala-2.12.tgz

    tar xzf ${MANGO_TMP_DIR}/${SPARK}-bin-without-hadoop-scala-2.12.tgz --directory ${MANGO_TMP_DIR}
    export SPARK_HOME=${MANGO_TMP_DIR}/${SPARK}-bin-without-hadoop-scala-2.12

    curl \
        -L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=hadoop/core/hadoop-2.7.7/hadoop-2.7.7.tar.gz" \
        -o ${MANGO_TMP_DIR}/hadoop-2.7.7.tar.gz

    tar xzf ${MANGO_TMP_DIR}/hadoop-2.7.7.tar.gz --directory ${MANGO_TMP_DIR}

    # remove references to avro 1.7.x
    find ${MANGO_TMP_DIR}/hadoop-2.7.7 -name *.jar | grep avro | xargs rm

    export SPARK_DIST_CLASSPATH=$(${MANGO_TMP_DIR}/hadoop-2.7.7/bin/hadoop classpath)
else
    curl \
        -v \
        -L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/${SPARK}/${SPARK}-bin-${HADOOP}.tgz" \
        -o ${MANGO_TMP_DIR}/${SPARK}-bin-${HADOOP}.tgz

    tar xzf ${MANGO_TMP_DIR}/${SPARK}-bin-${HADOOP}.tgz --directory ${MANGO_TMP_DIR}
    export SPARK_HOME=${MANGO_TMP_DIR}/${SPARK}-bin-${HADOOP}
fi
+ '[' 2.11 == 2.12 ']'
+ curl -v -L 'https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-2.4.6/spark-2.4.6-bin-hadoop2.7.tgz' -o /tmp/mangoTestaREF90A/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-hadoop2.7.tgz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying 95.216.24.32...
* TCP_NODELAY set
* Connected to www.apache.org (95.216.24.32) port 443 (#0)
* ALPN, offering h2
* ALPN, offering http/1.1
* Cipher selection: ALL:!EXPORT:!EXPORT40:!EXPORT56:!aNULL:!LOW:!RC4:@STRENGTH
* successfully set certificate verify locations:
*   CAfile: /etc/ssl/certs/ca-certificates.crt
  CApath: /etc/ssl/certs
* TLSv1.2 (OUT), TLS header, Certificate Status (22):
} [5 bytes data]
* TLSv1.2 (OUT), TLS handshake, Client hello (1):
} [512 bytes data]
* TLSv1.2 (IN), TLS handshake, Server hello (2):
{ [113 bytes data]
* TLSv1.2 (IN), TLS handshake, Certificate (11):
{ [4639 bytes data]
* TLSv1.2 (IN), TLS handshake, Server key exchange (12):
{ [333 bytes data]
* TLSv1.2 (IN), TLS handshake, Server finished (14):
{ [4 bytes data]
* TLSv1.2 (OUT), TLS handshake, Client key exchange (16):
} [70 bytes data]
* TLSv1.2 (OUT), TLS change cipher, Client hello (1):
} [1 bytes data]
* TLSv1.2 (OUT), TLS handshake, Finished (20):
} [16 bytes data]
* TLSv1.2 (IN), TLS change cipher, Client hello (1):
{ [1 bytes data]
* TLSv1.2 (IN), TLS handshake, Finished (20):
{ [16 bytes data]
* SSL connection using TLSv1.2 / ECDHE-RSA-AES256-GCM-SHA384
* ALPN, server accepted to use http/1.1
* Server certificate:
*  subject: OU=Domain Control Validated; OU=PositiveSSL Wildcard; CN=*.apache.org
*  start date: Jul  1 00:00:00 2019 GMT
*  expire date: Jun 30 23:59:59 2021 GMT
*  subjectAltName: host "www.apache.org" matched cert's "*.apache.org"
*  issuer: C=GB; ST=Greater Manchester; L=Salford; O=Sectigo Limited; CN=Sectigo RSA Domain Validation Secure Server CA
*  SSL certificate verify ok.
} [5 bytes data]
> GET /dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-2.4.6/spark-2.4.6-bin-hadoop2.7.tgz HTTP/1.1
> Host: www.apache.org
> User-Agent: curl/7.52.1
> Accept: */*
> 
{ [5 bytes data]
< HTTP/1.1 302 Found
< Date: Sun, 16 Aug 2020 22:16:12 GMT
< Server: Apache/2.4.18 (Ubuntu)
< Location: http://mirror.cc.columbia.edu/pub/software/apache/spark/spark-2.4.6/spark-2.4.6-bin-hadoop2.7.tgz
< Cache-Control: max-age=3600
< Expires: Sun, 16 Aug 2020 23:16:12 GMT
< Content-Length: 0
< 
* Curl_http_done: called premature == 0

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
* Connection #0 to host www.apache.org left intact
* Issue another request to this URL: 'http://mirror.cc.columbia.edu/pub/software/apache/spark/spark-2.4.6/spark-2.4.6-bin-hadoop2.7.tgz'
*   Trying 128.59.59.71...
* TCP_NODELAY set
* Connected to mirror.cc.columbia.edu (128.59.59.71) port 80 (#1)
> GET /pub/software/apache/spark/spark-2.4.6/spark-2.4.6-bin-hadoop2.7.tgz HTTP/1.1
> Host: mirror.cc.columbia.edu
> User-Agent: curl/7.52.1
> Accept: */*
> 
< HTTP/1.1 200 OK
< Date: Sun, 16 Aug 2020 22:15:44 GMT
< Server: Apache/2.2.22 (Fedora)
< Last-Modified: Sat, 30 May 2020 00:54:32 GMT
< ETag: "fce1580-de6945b-5a6d301334200"
< Accept-Ranges: bytes
< Content-Length: 233215067
< Content-Type: application/x-gzip
< 
{ [8432 bytes data]

  0  222M    0  8432    0     0   8797      0  7:21:50 --:--:--  7:21:50  8797
  0  222M    0  614k    0     0   314k      0  0:12:05  0:00:01  0:12:04  606k
  0  222M    0 1178k    0     0   375k      0  0:10:06  0:00:03  0:10:03  537k
  0  222M    0 1275k    0     0   320k      0  0:11:50  0:00:03  0:11:47  419k
  0  222M    0 1330k    0     0   265k      0  0:14:17  0:00:05  0:14:12  326k
  0  222M    0 1418k    0     0   237k      0  0:15:57  0:00:05  0:15:52  281k
  0  222M    0 1597k    0     0   229k      0  0:16:32  0:00:06  0:16:26  196k
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* Connection #1 to host mirror.cc.columbia.edu left intact
+ tar xzf /tmp/mangoTestaREF90A/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-hadoop2.7.tgz --directory /tmp/mangoTestaREF90A/deleteMePleaseThisIsNoLongerNeeded
+ export SPARK_HOME=/tmp/mangoTestaREF90A/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-hadoop2.7
+ SPARK_HOME=/tmp/mangoTestaREF90A/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-hadoop2.7

# run integration tests
# set the TMPDIR envar, which is used by python to choose where to make temp directories
export TMPDIR=${MANGO_TMP_DIR}
+ export TMPDIR=/tmp/mangoTestaREF90A/deleteMePleaseThisIsNoLongerNeeded
+ TMPDIR=/tmp/mangoTestaREF90A/deleteMePleaseThisIsNoLongerNeeded

pushd $PROJECT_ROOT
+ pushd /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts/..

# Copy the jar into our temp space for testing
cp -r . $MANGO_TMP_DIR
/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.6/label/ubuntu /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.6/label/ubuntu /home
+ cp -r . /tmp/mangoTestaREF90A/deleteMePleaseThisIsNoLongerNeeded
popd
+ popd

pushd $MANGO_TMP_DIR
+ pushd /tmp/mangoTestaREF90A/deleteMePleaseThisIsNoLongerNeeded
/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.6/label/ubuntu /home

# create a conda environment for python build, if necessary
/tmp/mangoTestaREF90A/deleteMePleaseThisIsNoLongerNeeded /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.6/label/ubuntu /home
pythons=( 3.6 )
+ pythons=(3.6)
for python in ${pythons[*]}
do
    set +x +v
    conda create -y -q -c conda-forge -n mango-build-${PYTHON_UUID} python=${python} pip=19.3.1 jupyterlab=2.0.1
    source activate mango-build-${PYTHON_UUID}
    set -x -v

    # install npm and node in the venv for mango-pileup
    conda install -y nodejs

    # prepare mango python
    pushd mango-python
    make prepare

    python -h
	make develop
    popd


    # we can run the python build, now that we have a spark executable
    # requires SPARK_HOME to be set
    mvn -U \
        -P python,distribution \
        package \
        -DskipTests \
        -Dhadoop.version=${HADOOP_VERSION} \
        -Dspark.version=${SPARK_VERSION}

    # clean mango python
    pushd mango-python
    make clean
    popd

    # prepare mango viz
    pushd mango-pileup
    make prepare
    popd

    # run the widgets tests (mango-pileup)
    mvn -P widgets test

    # clean mango viz
    pushd mango-pileup
    make clean
    popd

    # make sure that the distribution package contains an egg
    # if no assembly jar is found, this will exit with code 1 and fail the build
    tar tzf mango-distribution/target/mango-distribution*-bin.tar.gz | \
        grep bdgenomics.mango | \
        grep egg

    # test mango notebook, output to temporary log file
    MANGO_NOTEBOOK_LOGS=${MANGO_TMP_DIR}/mango-notebook.log

    # notebook args --ip=0.0.0.0 --no-browser --allow-root required for docker
    bash -xv ${PROJECT_ROOT}/bin/mango-notebook -- --ip=0.0.0.0 --no-browser --allow-root &> ${MANGO_NOTEBOOK_LOGS} &

    # sleep for 2 seconds to let mango-notebook start up
    sleep 2

    # if mango-notebook fails, then trying to kill the process will fail
    if kill $! ; then
        echo "Mango Notebook Succeeded"
    else
        echo "Mango Notebook failed with logs:"
        cat ${MANGO_NOTEBOOK_LOGS}
        exit 1
    fi

    # copy python targets back
    cp -r mango-python/target ${PROJECT_ROOT}/mango-python/

    # deactivate and remove the conda env
    set +e +x
    source deactivate
    conda remove -y --name mango-build-${PYTHON_UUID} --all
    set -e -x
done
+ for python in ${pythons[*]}
+ set +x +v
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1

  added / updated specs:
    - jupyterlab=2.0.1
    - pip=19.3.1
    - python=3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    _libgcc_mutex-0.1          |      conda_forge           3 KB  conda-forge
    _openmp_mutex-4.5          |            1_gnu          22 KB  conda-forge
    argon2-cffi-20.1.0         |   py36h8c4c3a4_1          47 KB  conda-forge
    attrs-19.3.0               |             py_0          35 KB  conda-forge
    backcall-0.2.0             |     pyh9f0ad1d_0          13 KB  conda-forge
    backports-1.0              |             py_2           4 KB  conda-forge
    backports.functools_lru_cache-1.6.1|             py_0           8 KB  conda-forge
    bleach-3.1.5               |     pyh9f0ad1d_0         112 KB  conda-forge
    brotlipy-0.7.0             |py36h8c4c3a4_1000         346 KB  conda-forge
    ca-certificates-2020.6.20  |       hecda079_0         145 KB  conda-forge
    certifi-2020.6.20          |   py36h9f0ad1d_0         151 KB  conda-forge
    cffi-1.14.1                |   py36h0ff685e_0         223 KB  conda-forge
    chardet-3.0.4              |py36h9f0ad1d_1006         188 KB  conda-forge
    cryptography-3.0           |   py36h45558ae_0         640 KB  conda-forge
    decorator-4.4.2            |             py_0          11 KB  conda-forge
    defusedxml-0.6.0           |             py_0          22 KB  conda-forge
    entrypoints-0.3            |py36h9f0ad1d_1001          12 KB  conda-forge
    idna-2.10                  |     pyh9f0ad1d_0          52 KB  conda-forge
    importlib-metadata-1.7.0   |   py36h9f0ad1d_0          44 KB  conda-forge
    importlib_metadata-1.7.0   |                0           3 KB  conda-forge
    ipykernel-5.3.4            |   py36h95af2a2_0         165 KB  conda-forge
    ipython-7.16.1             |   py36h95af2a2_0         1.1 MB  conda-forge
    ipython_genutils-0.2.0     |             py_1          21 KB  conda-forge
    jedi-0.17.2                |   py36h9f0ad1d_0         950 KB  conda-forge
    jinja2-2.11.2              |     pyh9f0ad1d_0          93 KB  conda-forge
    json5-0.9.4                |     pyh9f0ad1d_0          20 KB  conda-forge
    jsonschema-3.2.0           |   py36h9f0ad1d_1          89 KB  conda-forge
    jupyter_client-6.1.6       |             py_0          75 KB  conda-forge
    jupyter_core-4.6.3         |   py36h9f0ad1d_1          71 KB  conda-forge
    jupyterlab-2.0.1           |             py_0         5.7 MB  conda-forge
    jupyterlab_server-1.2.0    |             py_0          25 KB  conda-forge
    ld_impl_linux-64-2.34      |       hc38a660_9         612 KB  conda-forge
    libffi-3.2.1               |    he1b5a44_1007          47 KB  conda-forge
    libgcc-ng-9.3.0            |      h24d8f2e_15         7.8 MB  conda-forge
    libgomp-9.3.0              |      h24d8f2e_15         378 KB  conda-forge
    libsodium-1.0.18           |       h516909a_0         339 KB  conda-forge
    libstdcxx-ng-9.3.0         |      hdf63c60_15         4.0 MB  conda-forge
    markupsafe-1.1.1           |   py36h8c4c3a4_1          26 KB  conda-forge
    mistune-0.8.4              |py36h8c4c3a4_1001          53 KB  conda-forge
    nbconvert-5.6.1            |   py36h9f0ad1d_1         487 KB  conda-forge
    nbformat-5.0.7             |             py_0          99 KB  conda-forge
    ncurses-6.2                |       he1b5a44_1         993 KB  conda-forge
    notebook-6.1.3             |   py36h9f0ad1d_0         6.2 MB  conda-forge
    openssl-1.1.1g             |       h516909a_1         2.1 MB  conda-forge
    packaging-20.4             |     pyh9f0ad1d_0          32 KB  conda-forge
    pandoc-2.10.1              |       h516909a_0        19.3 MB  conda-forge
    pandocfilters-1.4.2        |             py_1           9 KB  conda-forge
    parso-0.7.1                |     pyh9f0ad1d_0          70 KB  conda-forge
    pexpect-4.8.0              |   py36h9f0ad1d_1          79 KB  conda-forge
    pickleshare-0.7.5          |py36h9f0ad1d_1001          13 KB  conda-forge
    pip-19.3.1                 |           py36_0         1.9 MB  conda-forge
    prometheus_client-0.8.0    |     pyh9f0ad1d_0          44 KB  conda-forge
    prompt-toolkit-3.0.6       |             py_0         235 KB  conda-forge
    ptyprocess-0.6.0           |          py_1001          15 KB  conda-forge
    pycparser-2.20             |     pyh9f0ad1d_2          94 KB  conda-forge
    pygments-2.6.1             |             py_0         683 KB  conda-forge
    pyopenssl-19.1.0           |             py_1          47 KB  conda-forge
    pyparsing-2.4.7            |     pyh9f0ad1d_0          60 KB  conda-forge
    pyrsistent-0.16.0          |   py36h8c4c3a4_0          89 KB  conda-forge
    pysocks-1.7.1              |   py36h9f0ad1d_1          27 KB  conda-forge
    python-3.6.11              |h4d41432_2_cpython        34.2 MB  conda-forge
    python-dateutil-2.8.1      |             py_0         220 KB  conda-forge
    python_abi-3.6             |          1_cp36m           4 KB  conda-forge
    pyzmq-19.0.2               |   py36h9947dbf_0         465 KB  conda-forge
    readline-8.0               |       he28a2e2_2         281 KB  conda-forge
    requests-2.24.0            |     pyh9f0ad1d_0          47 KB  conda-forge
    send2trash-1.5.0           |             py_0          12 KB  conda-forge
    setuptools-49.6.0          |   py36h9f0ad1d_0         935 KB  conda-forge
    six-1.15.0                 |     pyh9f0ad1d_0          14 KB  conda-forge
    sqlite-3.32.3              |       h4cf870e_1         1.4 MB  conda-forge
    terminado-0.8.3            |   py36h9f0ad1d_1          23 KB  conda-forge
    testpath-0.4.4             |             py_0          85 KB  conda-forge
    tk-8.6.10                  |       hed695b0_0         3.2 MB  conda-forge
    tornado-6.0.4              |   py36h8c4c3a4_1         639 KB  conda-forge
    traitlets-4.3.3            |   py36h9f0ad1d_1         133 KB  conda-forge
    urllib3-1.25.10            |             py_0          92 KB  conda-forge
    wcwidth-0.2.5              |     pyh9f0ad1d_1          33 KB  conda-forge
    webencodings-0.5.1         |             py_1          12 KB  conda-forge
    wheel-0.35.1               |     pyh9f0ad1d_0          29 KB  conda-forge
    xz-5.2.5                   |       h516909a_1         343 KB  conda-forge
    zeromq-4.3.2               |       he1b5a44_3         326 KB  conda-forge
    zipp-3.1.0                 |             py_0          10 KB  conda-forge
    zlib-1.2.11                |    h516909a_1007         106 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        98.7 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
  argon2-cffi        conda-forge/linux-64::argon2-cffi-20.1.0-py36h8c4c3a4_1
  attrs              conda-forge/noarch::attrs-19.3.0-py_0
  backcall           conda-forge/noarch::backcall-0.2.0-pyh9f0ad1d_0
  backports          conda-forge/noarch::backports-1.0-py_2
  backports.functoo~ conda-forge/noarch::backports.functools_lru_cache-1.6.1-py_0
  bleach             conda-forge/noarch::bleach-3.1.5-pyh9f0ad1d_0
  brotlipy           conda-forge/linux-64::brotlipy-0.7.0-py36h8c4c3a4_1000
  ca-certificates    conda-forge/linux-64::ca-certificates-2020.6.20-hecda079_0
  certifi            conda-forge/linux-64::certifi-2020.6.20-py36h9f0ad1d_0
  cffi               conda-forge/linux-64::cffi-1.14.1-py36h0ff685e_0
  chardet            conda-forge/linux-64::chardet-3.0.4-py36h9f0ad1d_1006
  cryptography       conda-forge/linux-64::cryptography-3.0-py36h45558ae_0
  decorator          conda-forge/noarch::decorator-4.4.2-py_0
  defusedxml         conda-forge/noarch::defusedxml-0.6.0-py_0
  entrypoints        conda-forge/linux-64::entrypoints-0.3-py36h9f0ad1d_1001
  idna               conda-forge/noarch::idna-2.10-pyh9f0ad1d_0
  importlib-metadata conda-forge/linux-64::importlib-metadata-1.7.0-py36h9f0ad1d_0
  importlib_metadata conda-forge/noarch::importlib_metadata-1.7.0-0
  ipykernel          conda-forge/linux-64::ipykernel-5.3.4-py36h95af2a2_0
  ipython            conda-forge/linux-64::ipython-7.16.1-py36h95af2a2_0
  ipython_genutils   conda-forge/noarch::ipython_genutils-0.2.0-py_1
  jedi               conda-forge/linux-64::jedi-0.17.2-py36h9f0ad1d_0
  jinja2             conda-forge/noarch::jinja2-2.11.2-pyh9f0ad1d_0
  json5              conda-forge/noarch::json5-0.9.4-pyh9f0ad1d_0
  jsonschema         conda-forge/linux-64::jsonschema-3.2.0-py36h9f0ad1d_1
  jupyter_client     conda-forge/noarch::jupyter_client-6.1.6-py_0
  jupyter_core       conda-forge/linux-64::jupyter_core-4.6.3-py36h9f0ad1d_1
  jupyterlab         conda-forge/noarch::jupyterlab-2.0.1-py_0
  jupyterlab_server  conda-forge/noarch::jupyterlab_server-1.2.0-py_0
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.34-hc38a660_9
  libffi             conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007
  libgcc-ng          conda-forge/linux-64::libgcc-ng-9.3.0-h24d8f2e_15
  libgomp            conda-forge/linux-64::libgomp-9.3.0-h24d8f2e_15
  libsodium          conda-forge/linux-64::libsodium-1.0.18-h516909a_0
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-9.3.0-hdf63c60_15
  markupsafe         conda-forge/linux-64::markupsafe-1.1.1-py36h8c4c3a4_1
  mistune            conda-forge/linux-64::mistune-0.8.4-py36h8c4c3a4_1001
  nbconvert          conda-forge/linux-64::nbconvert-5.6.1-py36h9f0ad1d_1
  nbformat           conda-forge/noarch::nbformat-5.0.7-py_0
  ncurses            conda-forge/linux-64::ncurses-6.2-he1b5a44_1
  notebook           conda-forge/linux-64::notebook-6.1.3-py36h9f0ad1d_0
  openssl            conda-forge/linux-64::openssl-1.1.1g-h516909a_1
  packaging          conda-forge/noarch::packaging-20.4-pyh9f0ad1d_0
  pandoc             conda-forge/linux-64::pandoc-2.10.1-h516909a_0
  pandocfilters      conda-forge/noarch::pandocfilters-1.4.2-py_1
  parso              conda-forge/noarch::parso-0.7.1-pyh9f0ad1d_0
  pexpect            conda-forge/linux-64::pexpect-4.8.0-py36h9f0ad1d_1
  pickleshare        conda-forge/linux-64::pickleshare-0.7.5-py36h9f0ad1d_1001
  pip                conda-forge/linux-64::pip-19.3.1-py36_0
  prometheus_client  conda-forge/noarch::prometheus_client-0.8.0-pyh9f0ad1d_0
  prompt-toolkit     conda-forge/noarch::prompt-toolkit-3.0.6-py_0
  ptyprocess         conda-forge/noarch::ptyprocess-0.6.0-py_1001
  pycparser          conda-forge/noarch::pycparser-2.20-pyh9f0ad1d_2
  pygments           conda-forge/noarch::pygments-2.6.1-py_0
  pyopenssl          conda-forge/noarch::pyopenssl-19.1.0-py_1
  pyparsing          conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0
  pyrsistent         conda-forge/linux-64::pyrsistent-0.16.0-py36h8c4c3a4_0
  pysocks            conda-forge/linux-64::pysocks-1.7.1-py36h9f0ad1d_1
  python             conda-forge/linux-64::python-3.6.11-h4d41432_2_cpython
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.1-py_0
  python_abi         conda-forge/linux-64::python_abi-3.6-1_cp36m
  pyzmq              conda-forge/linux-64::pyzmq-19.0.2-py36h9947dbf_0
  readline           conda-forge/linux-64::readline-8.0-he28a2e2_2
  requests           conda-forge/noarch::requests-2.24.0-pyh9f0ad1d_0
  send2trash         conda-forge/noarch::send2trash-1.5.0-py_0
  setuptools         conda-forge/linux-64::setuptools-49.6.0-py36h9f0ad1d_0
  six                conda-forge/noarch::six-1.15.0-pyh9f0ad1d_0
  sqlite             conda-forge/linux-64::sqlite-3.32.3-h4cf870e_1
  terminado          conda-forge/linux-64::terminado-0.8.3-py36h9f0ad1d_1
  testpath           conda-forge/noarch::testpath-0.4.4-py_0
  tk                 conda-forge/linux-64::tk-8.6.10-hed695b0_0
  tornado            conda-forge/linux-64::tornado-6.0.4-py36h8c4c3a4_1
  traitlets          conda-forge/linux-64::traitlets-4.3.3-py36h9f0ad1d_1
  urllib3            conda-forge/noarch::urllib3-1.25.10-py_0
  wcwidth            conda-forge/noarch::wcwidth-0.2.5-pyh9f0ad1d_1
  webencodings       conda-forge/noarch::webencodings-0.5.1-py_1
  wheel              conda-forge/noarch::wheel-0.35.1-pyh9f0ad1d_0
  xz                 conda-forge/linux-64::xz-5.2.5-h516909a_1
  zeromq             conda-forge/linux-64::zeromq-4.3.2-he1b5a44_3
  zipp               conda-forge/noarch::zipp-3.1.0-py_0
  zlib               conda-forge/linux-64::zlib-1.2.11-h516909a_1007


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ conda install -y nodejs
+ '[' 3 -lt 1 ']'
+ local cmd=install
+ shift
+ case "$cmd" in
+ CONDA_INTERNAL_OLDPATH=/opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ __add_sys_prefix_to_path
+ '[' -n '' ']'
++ dirname /opt/conda/bin/conda
+ SYSP=/opt/conda/bin
++ dirname /opt/conda/bin
+ SYSP=/opt/conda
+ '[' -n '' ']'
+ PATH=/opt/conda/bin:/opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ export PATH
+ /opt/conda/bin/conda install -y nodejs
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1

  added / updated specs:
    - nodejs


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2020.6.20          |           py36_0         156 KB
    ------------------------------------------------------------
                                           Total:         156 KB

The following NEW packages will be INSTALLED:

  nodejs             pkgs/main/linux-64::nodejs-10.13.0-he6710b0_0

The following packages will be UPDATED:

  ca-certificates    conda-forge::ca-certificates-2020.6.2~ --> pkgs/main::ca-certificates-2020.6.24-0

The following packages will be SUPERSEDED by a higher-priority channel:

  certifi            conda-forge::certifi-2020.6.20-py36h9~ --> pkgs/main::certifi-2020.6.20-py36_0
  openssl            conda-forge::openssl-1.1.1g-h516909a_1 --> pkgs/main::openssl-1.1.1g-h7b6447c_0



Downloading and Extracting Packages

certifi-2020.6.20    | 156 KB    |            |   0% 
certifi-2020.6.20    | 156 KB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ local t1=0
+ PATH=/opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ '[' 0 = 0 ']'
+ __conda_reactivate
+ local ask_conda
+ CONDA_INTERNAL_OLDPATH=/opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ __add_sys_prefix_to_path
+ '[' -n '' ']'
++ dirname /opt/conda/bin/conda
+ SYSP=/opt/conda/bin
++ dirname /opt/conda/bin
+ SYSP=/opt/conda
+ '[' -n '' ']'
+ PATH=/opt/conda/bin:/opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ export PATH
++ PS1='(mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1) '
++ /opt/conda/bin/conda shell.posix reactivate
+ ask_conda='PS1='\''(mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1) '\''
export PATH='\''/opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_SHLVL='\''1'\''
export CONDA_PROMPT_MODIFIER='\''(mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1) '\'''
+ PATH=/opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ eval 'PS1='\''(mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1) '\''
export PATH='\''/opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_SHLVL='\''1'\''
export CONDA_PROMPT_MODIFIER='\''(mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1) '\'''
PS1='(mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1) '
++ PS1='(mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1) '
export PATH='/opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'
++ export PATH=/opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ PATH=/opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
export CONDA_SHLVL='1'
++ export CONDA_SHLVL=1
++ CONDA_SHLVL=1
export CONDA_PROMPT_MODIFIER='(mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1) '
++ export 'CONDA_PROMPT_MODIFIER=(mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1) '
++ CONDA_PROMPT_MODIFIER='(mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1) '
+ __conda_hashr
+ '[' -n '' ']'
+ '[' -n '' ']'
+ hash -r
+ pushd mango-python
/tmp/mangoTestaREF90A/deleteMePleaseThisIsNoLongerNeeded/mango-python /tmp/mangoTestaREF90A/deleteMePleaseThisIsNoLongerNeeded /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.6/label/ubuntu /home
+ make prepare
pip install pytest==3.9.1
Collecting pytest==3.9.1
  Downloading https://files.pythonhosted.org/packages/bf/14/a16e1ac03aeb9776d98374bb76495a6623d56dff0f7b815ed5a1e04d893e/pytest-3.9.1-py2.py3-none-any.whl (213kB)
Collecting py>=1.5.0
  Downloading https://files.pythonhosted.org/packages/68/0f/41a43535b52a81e4f29e420a151032d26f08b62206840c48d14b70e53376/py-1.9.0-py2.py3-none-any.whl (99kB)
Requirement already satisfied: setuptools in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from pytest==3.9.1) (49.6.0.post20200814)
Collecting pluggy>=0.7
  Downloading https://files.pythonhosted.org/packages/a0/28/85c7aa31b80d150b772fbe4a229487bc6644da9ccb7e427dd8cc60cb8a62/pluggy-0.13.1-py2.py3-none-any.whl
Collecting atomicwrites>=1.0
  Downloading https://files.pythonhosted.org/packages/2c/a0/da5f49008ec6e9a658dbf5d7310a4debd397bce0b4db03cf8a410066bb87/atomicwrites-1.4.0-py2.py3-none-any.whl
Requirement already satisfied: six>=1.10.0 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from pytest==3.9.1) (1.15.0)
Collecting more-itertools>=4.0.0
  Downloading https://files.pythonhosted.org/packages/ef/9b/6c35ec5483710492e21252465160ee508170159f7e0e2d6cd769022f52f6/more_itertools-8.4.0-py3-none-any.whl (43kB)
Requirement already satisfied: attrs>=17.4.0 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from pytest==3.9.1) (19.3.0)
Requirement already satisfied: importlib-metadata>=0.12; python_version < "3.8" in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from pluggy>=0.7->pytest==3.9.1) (1.7.0)
Requirement already satisfied: zipp>=0.5 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from importlib-metadata>=0.12; python_version < "3.8"->pluggy>=0.7->pytest==3.9.1) (3.1.0)
Installing collected packages: py, pluggy, atomicwrites, more-itertools, pytest
Successfully installed atomicwrites-1.4.0 more-itertools-8.4.0 pluggy-0.13.1 py-1.9.0 pytest-3.9.1
# ipython version required for python 2.7
pip install jupyter_contrib_nbextensions
Collecting jupyter_contrib_nbextensions
  Downloading https://files.pythonhosted.org/packages/33/f0/6e2c00afda860f655fbf0f795f7310bdbf12122846344dfdc803fc7455d5/jupyter_contrib_nbextensions-0.5.1-py2.py3-none-any.whl (20.9MB)
Collecting jupyter-contrib-core>=0.3.3
  Downloading https://files.pythonhosted.org/packages/e6/8f/04a752a8b66a66e7092c035e5d87d2502ac7ec07f9fb6059059b6c0dc272/jupyter_contrib_core-0.3.3-py2.py3-none-any.whl
Collecting pyyaml
  Downloading https://files.pythonhosted.org/packages/64/c2/b80047c7ac2478f9501676c988a5411ed5572f35d1beff9cae07d321512c/PyYAML-5.3.1.tar.gz (269kB)
Requirement already satisfied: notebook>=4.0 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from jupyter_contrib_nbextensions) (6.1.3)
Requirement already satisfied: nbconvert>=4.2 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from jupyter_contrib_nbextensions) (5.6.1)
Requirement already satisfied: tornado in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from jupyter_contrib_nbextensions) (6.0.4)
Requirement already satisfied: jupyter-core in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from jupyter_contrib_nbextensions) (4.6.3)
Collecting lxml
  Downloading https://files.pythonhosted.org/packages/79/37/d420b7fdc9a550bd29b8cfeacff3b38502d9600b09d7dfae9a69e623b891/lxml-4.5.2-cp36-cp36m-manylinux1_x86_64.whl (5.5MB)
Requirement already satisfied: traitlets>=4.1 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from jupyter_contrib_nbextensions) (4.3.3)
Requirement already satisfied: ipython-genutils in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from jupyter_contrib_nbextensions) (0.2.0)
Collecting jupyter-highlight-selected-word>=0.1.1
  Downloading https://files.pythonhosted.org/packages/50/d7/19ab7cfd60bf268d2abbacc52d4295a40f52d74dfc0d938e4761ee5e598b/jupyter_highlight_selected_word-0.2.0-py2.py3-none-any.whl
Collecting jupyter-nbextensions-configurator>=0.4.0
  Downloading https://files.pythonhosted.org/packages/51/a3/d72d5f2dc10c5ccf5a6f4c79f636bf071a5ce462dedd07af2f70384db6cb/jupyter_nbextensions_configurator-0.4.1.tar.gz (479kB)
Collecting jupyter-latex-envs>=1.3.8
  Downloading https://files.pythonhosted.org/packages/0e/15/55805de080d5542f76920364635e96e64d3b37f678befdfe3b16aa154205/jupyter_latex_envs-1.4.6.tar.gz (861kB)
Requirement already satisfied: setuptools in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from jupyter-contrib-core>=0.3.3->jupyter_contrib_nbextensions) (49.6.0.post20200814)
Requirement already satisfied: jupyter-client>=5.3.4 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from notebook>=4.0->jupyter_contrib_nbextensions) (6.1.6)
Requirement already satisfied: ipykernel in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from notebook>=4.0->jupyter_contrib_nbextensions) (5.3.4)
Requirement already satisfied: prometheus-client in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from notebook>=4.0->jupyter_contrib_nbextensions) (0.8.0)
Requirement already satisfied: argon2-cffi in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from notebook>=4.0->jupyter_contrib_nbextensions) (20.1.0)
Requirement already satisfied: nbformat in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from notebook>=4.0->jupyter_contrib_nbextensions) (5.0.7)
Requirement already satisfied: terminado>=0.8.3 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from notebook>=4.0->jupyter_contrib_nbextensions) (0.8.3)
Requirement already satisfied: pyzmq>=17 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from notebook>=4.0->jupyter_contrib_nbextensions) (19.0.2)
Requirement already satisfied: jinja2 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from notebook>=4.0->jupyter_contrib_nbextensions) (2.11.2)
Requirement already satisfied: Send2Trash in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from notebook>=4.0->jupyter_contrib_nbextensions) (1.5.0)
Requirement already satisfied: pygments in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from nbconvert>=4.2->jupyter_contrib_nbextensions) (2.6.1)
Requirement already satisfied: bleach in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from nbconvert>=4.2->jupyter_contrib_nbextensions) (3.1.5)
Requirement already satisfied: mistune<2,>=0.8.1 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from nbconvert>=4.2->jupyter_contrib_nbextensions) (0.8.4)
Requirement already satisfied: pandocfilters>=1.4.1 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from nbconvert>=4.2->jupyter_contrib_nbextensions) (1.4.2)
Requirement already satisfied: testpath in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from nbconvert>=4.2->jupyter_contrib_nbextensions) (0.4.4)
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Requirement already satisfied: zipp>=0.5 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from importlib-metadata; python_version < "3.8"->jsonschema!=2.5.0,>=2.4->nbformat->notebook>=4.0->jupyter_contrib_nbextensions) (3.1.0)
Building wheels for collected packages: pyyaml, jupyter-nbextensions-configurator, jupyter-latex-envs
  Building wheel for pyyaml (setup.py): started
  Building wheel for pyyaml (setup.py): finished with status 'done'
  Created wheel for pyyaml: filename=PyYAML-5.3.1-cp36-cp36m-linux_x86_64.whl size=44619 sha256=d1e4b65d5f476171e8fec0522b7090a8bda7f3d1e87a19938391aeee6f2dfbc2
  Stored in directory: /root/.cache/pip/wheels/a7/c1/ea/cf5bd31012e735dc1dfea3131a2d5eae7978b251083d6247bd
  Building wheel for jupyter-nbextensions-configurator (setup.py): started
  Building wheel for jupyter-nbextensions-configurator (setup.py): finished with status 'done'
  Created wheel for jupyter-nbextensions-configurator: filename=jupyter_nbextensions_configurator-0.4.1-py2.py3-none-any.whl size=465825 sha256=528ec47b4e41c47b3b856b233a2742d20cf385998c3078247d675cf6b860416b
  Stored in directory: /root/.cache/pip/wheels/15/df/fe/2a74fe34709e7fdc5ae153a768675d9fda93cc7d5133ed1fb0
  Building wheel for jupyter-latex-envs (setup.py): started
  Building wheel for jupyter-latex-envs (setup.py): finished with status 'done'
  Created wheel for jupyter-latex-envs: filename=jupyter_latex_envs-1.4.6-py2.py3-none-any.whl size=963395 sha256=f8f40b67d5dceecf08bcf8b523a122826eae151a14e822f4fb6380634dab478d
  Stored in directory: /root/.cache/pip/wheels/0d/71/2a/164491997299b9f2479a251e254323fe35d946779e18f27956
Successfully built pyyaml jupyter-nbextensions-configurator jupyter-latex-envs
Installing collected packages: jupyter-contrib-core, pyyaml, lxml, jupyter-highlight-selected-word, jupyter-nbextensions-configurator, jupyter-latex-envs, jupyter-contrib-nbextensions
Successfully installed jupyter-contrib-core-0.3.3 jupyter-contrib-nbextensions-0.5.1 jupyter-highlight-selected-word-0.2.0 jupyter-latex-envs-1.4.6 jupyter-nbextensions-configurator-0.4.1 lxml-4.5.2 pyyaml-5.3.1
pip install -r requirements.txt
Collecting cigar==0.1.3
  Downloading https://files.pythonhosted.org/packages/2d/5f/ffa58a8c64f811772b69a01eeab25c602b72d02a0c83006177c21abedaa3/cigar-0.1.3.tar.gz
Collecting matplotlib==2.0.2
  Downloading https://files.pythonhosted.org/packages/60/d4/6b6d8a7a6bc69a1602ab372f6fc6e88ef88a8a96398a1a25edbac636295b/matplotlib-2.0.2-cp36-cp36m-manylinux1_x86_64.whl (14.6MB)
Collecting ipython==7.8.0
  Downloading https://files.pythonhosted.org/packages/fb/44/f28a13852e562af719f9de1761680a84a93e8b4c50e22d00d68f60ee2e8b/ipython-7.8.0-py3-none-any.whl (775kB)
Collecting jupyter==1.0.0
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Collecting bdgenomics.adam==0.30.0
  Downloading https://files.pythonhosted.org/packages/8d/4b/b5b92dedae5ddd4e6f425f40a61332a3f646ac4616f840262ebb9441d396/bdgenomics.adam-0.30.0.tar.gz (39.5MB)
Collecting bdgenomics.mango.pileup==0.0.6a0
  Downloading https://files.pythonhosted.org/packages/48/8f/06f3e694caf8ba67dadbfca5c7f050343e7e3363ba348d94a224aa964cfb/bdgenomics.mango.pileup-0.0.6a0.tar.gz (892kB)
Collecting ipywidgets==7.0.0
  Downloading https://files.pythonhosted.org/packages/14/ea/793f6588d5be295d103fb868e26ba8671686b70bd855a21d02302f8dcd37/ipywidgets-7.0.0-py2.py3-none-any.whl (64kB)
Collecting psutil
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Requirement already satisfied: six>=1.10 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (1.15.0)
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Collecting numpy>=1.7.1
  Downloading https://files.pythonhosted.org/packages/b1/9a/7d474ba0860a41f771c9523d8c4ea56b084840b5ca4092d96bdee8a3b684/numpy-1.19.1-cp36-cp36m-manylinux2010_x86_64.whl (14.5MB)
Collecting pytz
  Downloading https://files.pythonhosted.org/packages/4f/a4/879454d49688e2fad93e59d7d4efda580b783c745fd2ec2a3adf87b0808d/pytz-2020.1-py2.py3-none-any.whl (510kB)
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Collecting cycler>=0.10
  Downloading https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
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Collecting prompt-toolkit<2.1.0,>=2.0.0
  Downloading https://files.pythonhosted.org/packages/87/61/2dfea88583d5454e3a64f9308a686071d58d59a55db638268a6413e1eb6d/prompt_toolkit-2.0.10-py3-none-any.whl (340kB)
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Collecting jupyter-console
  Downloading https://files.pythonhosted.org/packages/0a/89/742fa5a80b552ffcb6a8922712697c6e6828aee7b91ee4ae2b79f00f8401/jupyter_console-6.1.0-py2.py3-none-any.whl
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Collecting qtconsole
  Downloading https://files.pythonhosted.org/packages/42/63/08c241c351d527089083002f65905b81457fc5849fb87cafb08f2a00b354/qtconsole-4.7.5-py2.py3-none-any.whl (118kB)
Collecting pyspark>=1.6.0
  Downloading https://files.pythonhosted.org/packages/8e/b0/bf9020b56492281b9c9d8aae8f44ff51e1bc91b3ef5a884385cb4e389a40/pyspark-3.0.0.tar.gz (204.7MB)
Collecting modin[ray]==0.6.1
  Downloading https://files.pythonhosted.org/packages/4f/62/dbea5f16c685aa1bab65787562f4990d5b78caa915c7d323b47013c454ad/modin-0.6.1-py3-none-any.whl (230kB)
Collecting pytest==2.8.3
  Downloading https://files.pythonhosted.org/packages/b0/7b/7aa01fa919ca0d038cdf8744ba9fd0416b04ec1878a68bfd77f39534e408/pytest-2.8.3-py2.py3-none-any.whl (149kB)
Collecting widgetsnbextension~=3.0.0
  Downloading https://files.pythonhosted.org/packages/8d/f2/c8bcccccbed39d51d3e237fb0c0f0c9bbc845d12afc41f5ca5f5728fffc7/widgetsnbextension-3.0.8-py2.py3-none-any.whl (2.2MB)
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Requirement already satisfied: bleach in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (3.1.5)
Requirement already satisfied: tornado>=4.2 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from ipykernel->jupyter==1.0.0->-r requirements.txt (line 4)) (6.0.4)
Requirement already satisfied: jupyter-client in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from ipykernel->jupyter==1.0.0->-r requirements.txt (line 4)) (6.1.6)
Requirement already satisfied: terminado>=0.8.3 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (0.8.3)
Requirement already satisfied: prometheus-client in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (0.8.0)
Requirement already satisfied: argon2-cffi in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (20.1.0)
Requirement already satisfied: Send2Trash in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (1.5.0)
Requirement already satisfied: pyzmq>=17 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (19.0.2)
Collecting qtpy
  Downloading https://files.pythonhosted.org/packages/cd/fd/9972948f02e967b691cc0ca1f26124826a3b88cb38f412a8b7935b8c3c72/QtPy-1.9.0-py2.py3-none-any.whl (54kB)
Collecting py4j==0.10.9
  Downloading https://files.pythonhosted.org/packages/9e/b6/6a4fb90cd235dc8e265a6a2067f2a2c99f0d91787f06aca4bcf7c23f3f80/py4j-0.10.9-py2.py3-none-any.whl (198kB)
Collecting pandas==0.25.1
  Downloading https://files.pythonhosted.org/packages/73/9b/52e228545d14f14bb2a1622e225f38463c8726645165e1cb7dde95bfe6d4/pandas-0.25.1-cp36-cp36m-manylinux1_x86_64.whl (10.5MB)
Collecting ray==0.7.3; extra == "ray"
  Downloading https://files.pythonhosted.org/packages/a7/21/de080b8458de41fd8ac20dd96547418c0ed94eab4359e5885f4041d61337/ray-0.7.3-cp36-cp36m-manylinux1_x86_64.whl (48.5MB)
Requirement already satisfied: py>=1.4.29 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from pytest==2.8.3->bdgenomics.mango.pileup==0.0.6a0->-r requirements.txt (line 6)) (1.9.0)
Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 7)) (3.2.0)
Requirement already satisfied: MarkupSafe>=0.23 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from jinja2>=2.4->nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (1.1.1)
Requirement already satisfied: packaging in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from bleach->nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (20.4)
Requirement already satisfied: webencodings in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from bleach->nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.5.1)
Requirement already satisfied: cffi>=1.0.0 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from argon2-cffi->notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (1.14.1)
Requirement already satisfied: pyyaml in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a0->-r requirements.txt (line 6)) (5.3.1)
Collecting click
  Downloading https://files.pythonhosted.org/packages/d2/3d/fa76db83bf75c4f8d338c2fd15c8d33fdd7ad23a9b5e57eb6c5de26b430e/click-7.1.2-py2.py3-none-any.whl (82kB)
Collecting redis
  Downloading https://files.pythonhosted.org/packages/a7/7c/24fb0511df653cf1a5d938d8f5d19802a88cef255706fdda242ff97e91b7/redis-3.5.3-py2.py3-none-any.whl (72kB)
Collecting protobuf>=3.8.0
  Downloading https://files.pythonhosted.org/packages/30/79/510974552cebff2ba04038544799450defe75e96ea5f1675dbf72cc8744f/protobuf-3.13.0-cp36-cp36m-manylinux1_x86_64.whl (1.3MB)
Collecting filelock
  Downloading https://files.pythonhosted.org/packages/93/83/71a2ee6158bb9f39a90c0dea1637f81d5eef866e188e1971a1b1ab01a35a/filelock-3.0.12-py3-none-any.whl
Collecting funcsigs
  Downloading https://files.pythonhosted.org/packages/69/cb/f5be453359271714c01b9bd06126eaf2e368f1fddfff30818754b5ac2328/funcsigs-1.0.2-py2.py3-none-any.whl
Collecting colorama
  Downloading https://files.pythonhosted.org/packages/c9/dc/45cdef1b4d119eb96316b3117e6d5708a08029992b2fee2c143c7a0a5cc5/colorama-0.4.3-py2.py3-none-any.whl
Requirement already satisfied: importlib-metadata; python_version < "3.8" in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 7)) (1.7.0)
Requirement already satisfied: attrs>=17.4.0 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 7)) (19.3.0)
Requirement already satisfied: pyrsistent>=0.14.0 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 7)) (0.16.0)
Requirement already satisfied: pycparser in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from cffi>=1.0.0->argon2-cffi->notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (2.20)
Requirement already satisfied: zipp>=0.5 in /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/lib/python3.6/site-packages (from importlib-metadata; python_version < "3.8"->jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 7)) (3.1.0)
Building wheels for collected packages: cigar, bdgenomics.adam, bdgenomics.mango.pileup, psutil, pyspark
  Building wheel for cigar (setup.py): started
  Building wheel for cigar (setup.py): finished with status 'done'
  Created wheel for cigar: filename=cigar-0.1.3-cp36-none-any.whl size=4024 sha256=22d54a74797239bc75cfebc788cb0d55f53f044d32d9d550964ea6c9358b7acc
  Stored in directory: /root/.cache/pip/wheels/eb/c0/e6/f0f525ada263f7f72f4b3efcc7f5b3c12a372f07f55a2d687d
  Building wheel for bdgenomics.adam (setup.py): started
  Building wheel for bdgenomics.adam (setup.py): finished with status 'done'
  Created wheel for bdgenomics.adam: filename=bdgenomics.adam-0.30.0-cp36-none-any.whl size=39575669 sha256=48844c955812d2b91de9e8debc68c28a51bdf84587cf3d70b63717d3decd0d3a
  Stored in directory: /root/.cache/pip/wheels/06/70/62/114cc2bb8d85bfc915d4571adb8f94cc558fdeef2bc09d61ee
  Building wheel for bdgenomics.mango.pileup (setup.py): started
  Building wheel for bdgenomics.mango.pileup (setup.py): finished with status 'done'
  Created wheel for bdgenomics.mango.pileup: filename=bdgenomics.mango.pileup-0.0.6a0-cp36-none-any.whl size=1798435 sha256=63941ac9effc82059fd3f0daf53ca64ffa6fc924a486ef3dbcaabe435a59038a
  Stored in directory: /root/.cache/pip/wheels/ec/df/8e/7e6efc45fd34e2850763a5ec5ac7f27052424d26105f12f971
  Building wheel for psutil (setup.py): started
  Building wheel for psutil (setup.py): finished with status 'done'
  Created wheel for psutil: filename=psutil-5.7.2-cp36-cp36m-linux_x86_64.whl size=279865 sha256=15888852c27d64ffe937fd789f58def609e66b27ceff6718e89e47efa97afc35
  Stored in directory: /root/.cache/pip/wheels/39/a0/f5/c4fa280463e29aea07797acb5312358fefb067c1f4f98e11b1
  Building wheel for pyspark (setup.py): started
  Building wheel for pyspark (setup.py): finished with status 'done'
  Created wheel for pyspark: filename=pyspark-3.0.0-py2.py3-none-any.whl size=205044184 sha256=d5634aeb67f8a684d07ca99e558c220496d4a33249fd04fb0cd18c4618066230
  Stored in directory: /root/.cache/pip/wheels/57/27/4d/ddacf7143f8d5b76c45c61ee2e43d9f8492fc5a8e78ebd7d37
Successfully built cigar bdgenomics.adam bdgenomics.mango.pileup psutil pyspark
ERROR: bdgenomics-mango-pileup 0.0.6a0 has requirement six==1.11.0, but you'll have six 1.15.0 which is incompatible.
Installing collected packages: cigar, numpy, pytz, cycler, matplotlib, prompt-toolkit, ipython, jupyter-console, widgetsnbextension, ipywidgets, qtpy, qtconsole, jupyter, py4j, pyspark, bdgenomics.adam, pandas, click, redis, pytest, protobuf, filelock, funcsigs, colorama, ray, modin, bdgenomics.mango.pileup, psutil
  Found existing installation: prompt-toolkit 3.0.6
    Uninstalling prompt-toolkit-3.0.6:
      Successfully uninstalled prompt-toolkit-3.0.6
  Found existing installation: ipython 7.16.1
    Uninstalling ipython-7.16.1:
      Successfully uninstalled ipython-7.16.1
  Found existing installation: pytest 3.9.1
    Uninstalling pytest-3.9.1:
      Successfully uninstalled pytest-3.9.1
Successfully installed bdgenomics.adam-0.30.0 bdgenomics.mango.pileup-0.0.6a0 cigar-0.1.3 click-7.1.2 colorama-0.4.3 cycler-0.10.0 filelock-3.0.12 funcsigs-1.0.2 ipython-7.8.0 ipywidgets-7.0.0 jupyter-1.0.0 jupyter-console-6.1.0 matplotlib-2.0.2 modin-0.6.1 numpy-1.19.1 pandas-0.25.1 prompt-toolkit-2.0.10 protobuf-3.13.0 psutil-5.7.2 py4j-0.10.9 pyspark-3.0.0 pytest-2.8.3 pytz-2020.1 qtconsole-4.7.5 qtpy-1.9.0 ray-0.7.3 redis-3.5.3 widgetsnbextension-3.0.8
+ python -h
/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts/jenkins-test: line 230: /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1/bin/python: Invalid argument
clean_up
+ clean_up
+ set +x +v
DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'.

## Package Plan ##

  environment location: /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1


The following packages will be REMOVED:

  _libgcc_mutex-0.1-conda_forge
  _openmp_mutex-4.5-1_gnu
  argon2-cffi-20.1.0-py36h8c4c3a4_1
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  mistune-0.8.4-py36h8c4c3a4_1001
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  nodejs-10.13.0-he6710b0_0
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  ptyprocess-0.6.0-py_1001
  pycparser-2.20-pyh9f0ad1d_2
  pygments-2.6.1-py_0
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  pyrsistent-0.16.0-py36h8c4c3a4_0
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  python-3.6.11-h4d41432_2_cpython
  python-dateutil-2.8.1-py_0
  python_abi-3.6-1_cp36m
  pyzmq-19.0.2-py36h9947dbf_0
  readline-8.0-he28a2e2_2
  requests-2.24.0-pyh9f0ad1d_0
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  six-1.15.0-pyh9f0ad1d_0
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  xz-5.2.5-h516909a_1
  zeromq-4.3.2-he1b5a44_3
  zipp-3.1.0-py_0
  zlib-1.2.11-h516909a_1007


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done

Remove all packages in environment /opt/conda/envs/mango-build-27e85a19-e762-46c7-9efb-2576f6bbb5c1:

Build step 'Execute shell' marked build as failure
Finished: FAILURE